Since MolTrans  uses sequential sub-structures, we also include a positional embedding \({\mathbf {E}^\mathrm {p}_\mathrm {pos}}_i, {\mathbf {E}^\mathrm {d}_\mathrm {pos}}_j\) 
via a lookup dictionary [1]} \(\mathbf {W}^\mathrm {p}_\mathrm {pos} \in \mathbb {R}^{\vartheta \times \Theta _p}\)  and \(\mathbf {W}^\mathrm {d}_\mathrm {pos} \in \mathbb {R}^{\vartheta \times \Theta _d}\) :
\({\mathbf {E}^\mathrm {p}_\mathrm {pos}}_i = \mathbf {W}^\mathrm {p}_\mathrm {pos} \mathbb {I}^\mathrm {p}_i, \hspace{5.69054pt} {\mathbf {E}^\mathrm {d}_\mathrm {pos}}_j = \mathbf {W}^\mathrm {d}_\mathrm {pos} \mathbb {I}^\mathrm {d}_j,\) 
